Recent information has revealed the functional diversity and importance of mitochondria in many cellular processes including orchestrating the innate immune response. Intriguingly, several infectious agents, such as Toxoplasma, Legionella, and Chlamydia, have been reported to grow within vacuoles surrounded by host mitochondria. Although many hypotheses have been proposed for the existence of host mitochondrial association (HMA), the causes and biological consequences of HMA have remained unanswered. Here we show that HMA is present in type I and III strains of Toxoplasma but missing in type II strains, both in vitro and in vivo. Analysis of F1 progeny from a type IIxIII cross revealed that HMA is a Mendelian trait that we could map. We use bioinformatics to select potential candidates and experimentally identify the polymorphic parasite protein involved, mitochondrial association factor 1 (MAF1). We show that introducing the type I (HMA(+)) MAF1 allele into type II (HMA(-)) parasites results in conversion to HMA(+) and deletion of MAF1 in type I parasites results in a loss of HMA. We observe that the loss and gain of HMA are associated with alterations in the transcription of host cell immune genes and the in vivo cytokine response during murine infection. Lastly, we use exogenous expression of MAF1 to show that it binds host mitochondria and thus MAF1 is the parasite protein directly responsible for HMA. Our findings suggest that association with host mitochondria may represent a novel means by which Toxoplasma tachyzoites manipulate the host. The existence of naturally occurring HMA(+) and HMA(-) strains of Toxoplasma, Legionella, and Chlamydia indicates the existence of evolutionary niches where HMA is either advantageous or disadvantageous, likely reflecting tradeoffs in metabolism, immune regulation, and other functions of mitochondria. Author Summary Recent discoveries have revealed the remarkable functional diversity of mitochondria in roles other than energy production, including an integral role for mitochondria and their dynamics in the regulation of the innate immune response. Interestingly, host mitochondria are recruited to the membranes that surround certain intracellular bacteria and parasites during infection. To date, how and why this phenomenon occurs has been a mystery, although it has been proposed to provide a metabolic benefit to the microbes. Here we identify mitochondrial association factor 1 (MAF1) as the parasite protein that mediates the association between the protozoan pathogen Toxoplasma and host mitochondria during infection. We show that MAF1 is needed to recruit host mitochondria to the Toxoplasma-containing vacuole and that this process is associated with changes in the immune response in infected cells and animals. These findings show that recruitment and association with host mitochondria is an important means by which intracellular pathogens interface with their host. We also find that the cost-benefit outcome of altering mitochondrial function might differ between strains depending on the precise niche in which they evolved; for infectious agents, these differences likely reflect different host organisms.